SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    349736, 349943, 358420, 355716, 351470, 
    352364, 354432, 354737, 358745, 349826, 
    352111, 352597, 354793, 355136, 358867, 
    359065, 352613, 354825, 357476, 354601, 
    356325, 359419, 351436, 352333, 354866, 
    355987, 356197, 351538, 351595, 354545, 
    355124, 355811, 358485, 358866, 349896, 
    351591, 352307, 355889, 352480, 352507, 
    356296, 356615, 357642, 358415, 351551, 
    355742, 357553, 359053, 351448, 352528, 
    354847, 355899, 356640, 359091, 352724, 
    354785, 352671, 358340, 352149, 352672, 
    353117, 357503, 352217, 352560, 356354, 
    356586, 352556, 355069, 355667, 352670, 
    349905, 356488, 358706, 349816, 351266, 
    352110, 352212, 352475, 352344, 352504, 
    352721, 354787, 355097, 355903, 355937, 
    356238, 356448, 351347, 351354, 351820, 
    352134, 352727, 354376, 356478, 358976, 
    359011, 352476, 352557, 352594, 352756
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00306

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "280.31"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 200,
        "rows_produced_per_join": 200,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "240.31",
          "eval_cost": "40.00",
          "prefix_cost": "280.31",
          "data_read_per_join": "12K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (349736,349943,358420,355716,351470,352364,354432,354737,358745,349826,352111,352597,354793,355136,358867,359065,352613,354825,357476,354601,356325,359419,351436,352333,354866,355987,356197,351538,351595,354545,355124,355811,358485,358866,349896,351591,352307,355889,352480,352507,356296,356615,357642,358415,351551,355742,357553,359053,351448,352528,354847,355899,356640,359091,352724,354785,352671,358340,352149,352672,353117,357503,352217,352560,356354,356586,352556,355069,355667,352670,349905,356488,358706,349816,351266,352110,352212,352475,352344,352504,352721,354787,355097,355903,355937,356238,356448,351347,351354,351820,352134,352727,354376,356478,358976,359011,352476,352557,352594,352756)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}